def test_fit_arrhenius(self):
Ea = 0.5
k = const.k / const.e
c = 12
temps = np.array([300, 1000, 500])
diffusivities = c * np.exp(-Ea / (k * temps))
diffusivities *= np.array([1.00601834013, 1.00803236262, 0.98609720824])
r = fit_arrhenius(temps, diffusivities)
self.assertAlmostEqual(r[0], Ea)
self.assertAlmostEqual(r[1], c)
self.assertAlmostEqual(r[2], 0.000895566)
# when not enough values for error estimate
r2 = fit_arrhenius([1, 2], [10, 10])
self.assertAlmostEqual(r2[0], 0)
self.assertAlmostEqual(r2[1], 10)
self.assertEqual(r2[2], None)
def test_fit_arrhenius(self):
Ea = 0.5
k = phyc.k_b / phyc.e
c = 12
temps = np.array([300, 1000, 500])
diffusivities = c * np.exp(-Ea / (k * temps))
r = fit_arrhenius(temps, diffusivities)
self.assertAlmostEqual(r[0], Ea)
self.assertAlmostEqual(r[1], c)
def test_fit_arrhenius(self):
Ea = 0.5
k = phyc.k_b / phyc.e
c = 12
temps = np.array([300, 1000, 500])
diffusivities = c * np.exp(-Ea/(k * temps))
r = fit_arrhenius(temps, diffusivities)
self.assertAlmostEqual(r[0], Ea)
self.assertAlmostEqual(r[1], c)
def test_fit_arrhenius(self):
Ea = 0.5
k = const.k / const.e
c = 12
temps = np.array([300, 1000, 500])
diffusivities = c * np.exp(-Ea/(k * temps))
diffusivities *= np.array([1.00601834013,
1.00803236262,
0.98609720824])
r = fit_arrhenius(temps, diffusivities)
self.assertAlmostEqual(r[0], Ea)
self.assertAlmostEqual(r[1], c)
self.assertAlmostEqual(r[2], 0.000895566)
# when not enough values for error estimate
r2 = fit_arrhenius([1, 2], [10, 10])
self.assertAlmostEqual(r2[0], 0)
self.assertAlmostEqual(r2[1], 10)
self.assertEqual(r2[2], None)
def Diffusion(self, skip=10, spaces='S', temp=[300, 310, 350, 390]):
from pymatgen.analysis.diffusion_analyzer import DiffusionAnalyzer, fit_arrhenius, get_arrhenius_plot
import shutil
import os
os.chdir(self.dire)
filePath = self.dire
file = []
for dirpath, dirnames, filenames in os.walk(filePath):
# print(dirpath)
for name in dirnames:
path = os.path.join(filePath, name)
path1 = os.path.join(path, 'vasprun.xml')
print(path1)
file.append(str(path1))
diff = DiffusionAnalyzer.from_files(file,
specie=spaces,
step_skip=skip)
diff.get_msd_plot()
diff.get_summary_dict()
fit = fit_arrhenius(temps=temp, diffusivities=diff.diffusivity)
plot = get_arrhenius_plot(temps=temp, diffusivities=diff.diffusivity)
